The main aim of present investigation was to study the oxidation products of nucleosides and nucleotides with the use of on-line electrochemistry/electrospray ionization mass spectrometry (EC-ESI-MS) system. The conditions applied in the system were optimized in complex manner, involving study of the impact of working electrodes or sample solvent on the oxidation of tested compounds and their ionization in mass spectrometry. Finally 5mM of ammonium acetate was used selected and pH 3 was used for positive ionization mode, while pH 7 was applied for negative ionization in mass spectrometry. It was shown that utilization of both ionization modes is indispensable in order to detect and identify all of oxidation products. Furthermore the identification of compounds obtained using the EC-ESI-MS system was done and results were compared with known metabolites of studied compounds. These products are associated with specific disease states, or may be a potential metabolites. Moreover the analysis of urine samples by liquid chromatography coupled with mass spectrometry confirmed the possibility of using EC-ESI-MS technique to simulate the metabolism of nucleosides and nucleotides, since the oxidation products have also been identified in urine samples.